Package org.biojava.bio.seq.io

Class GenbankFormat

  • All Implemented Interfaces:
    java.io.Serializable, java.util.EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource
    Direct Known Subclasses:
    GenbankXmlFormat, GenpeptFormat
    public class GenbankFormat
extends java.lang.Object
implements SequenceFormat, java.io.Serializable, ParseErrorListener, ParseErrorSource
    Deprecated.
    Use org.biojavax.bio.seq.io.GenbankFormat
    Format reader for GenBank files. Converted from the old style io to the new by working from EmblLikeFormat.
    Author:
    Thomas Down, Thad Welch Added GenBank header info to the sequence annotation. The ACCESSION header tag is not included. Stored in sequence.getName()., Greg Cox, Keith James, Matthew Pocock, Ron Kuhn
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static java.lang.String ACCESSION_TAG
      Deprecated.
       
      protected static java.lang.String AUTHORS_TAG
      Deprecated.
       
      protected static java.lang.String BASE_COUNT_TAG
      Deprecated.
       
      protected static java.lang.String CIRCULAR_TAG
      Deprecated.
       
      protected static java.lang.String COMMENT_TAG
      Deprecated.
       
      protected static java.lang.String COORDINATE_TAG
      Deprecated.
       
      protected static java.lang.String DATE_TAG
      Deprecated.
       
      static java.lang.String DEFAULT
      Deprecated.
       
      protected static java.lang.String DEFINITION_TAG
      Deprecated.
       
      protected static java.lang.String DIVISION_TAG
      Deprecated.
       
      protected static java.lang.String END_SEQUENCE_TAG
      Deprecated.
       
      protected static java.lang.String FEATURE_FLAG
      Deprecated.
       
      protected static java.lang.String FEATURE_LINE_PREFIX
      Deprecated.
       
      protected static java.lang.String FEATURE_TAG
      Deprecated.
       
      protected static java.lang.String GI_TAG
      Deprecated.
       
      protected static java.lang.String JOURNAL_TAG
      Deprecated.
       
      protected static java.lang.String KEYWORDS_TAG
      Deprecated.
       
      protected static java.lang.String LOCUS_TAG
      Deprecated.
       
      protected static java.lang.String MEDLINE_TAG
      Deprecated.
       
      protected static java.lang.String ORGANISM_TAG
      Deprecated.
       
      protected static java.lang.String PUBMED_TAG
      Deprecated.
       
      protected static java.lang.String REF_ACCESSION_TAG
      Deprecated.
       
      protected static java.lang.String REFERENCE_TAG
      Deprecated.
       
      protected static java.lang.String SIZE_TAG
      Deprecated.
       
      protected static java.lang.String SOURCE_TAG
      Deprecated.
       
      protected static java.lang.String START_SEQUENCE_TAG
      Deprecated.
       
      protected static java.lang.String STRAND_NUMBER_TAG
      Deprecated.
       
      protected static java.lang.String TITLE_TAG
      Deprecated.
       
      protected static java.lang.String TYPE_TAG
      Deprecated.
       
      protected static java.lang.String VERSION_TAG
      Deprecated.
       

    • Constructor Summary

      Constructors 
      Constructor Description
      GenbankFormat()
      Deprecated.
       

    • Field Detail

      • LOCUS_TAG

        protected static final java.lang.String LOCUS_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • STRAND_NUMBER_TAG

        protected static final java.lang.String STRAND_NUMBER_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • CIRCULAR_TAG

        protected static final java.lang.String CIRCULAR_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • DIVISION_TAG

        protected static final java.lang.String DIVISION_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • ACCESSION_TAG

        protected static final java.lang.String ACCESSION_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • VERSION_TAG

        protected static final java.lang.String VERSION_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • KEYWORDS_TAG

        protected static final java.lang.String KEYWORDS_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • DEFINITION_TAG

        protected static final java.lang.String DEFINITION_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • SOURCE_TAG

        protected static final java.lang.String SOURCE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • ORGANISM_TAG

        protected static final java.lang.String ORGANISM_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • REFERENCE_TAG

        protected static final java.lang.String REFERENCE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • COORDINATE_TAG

        protected static final java.lang.String COORDINATE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • REF_ACCESSION_TAG

        protected static final java.lang.String REF_ACCESSION_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • AUTHORS_TAG

        protected static final java.lang.String AUTHORS_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • TITLE_TAG

        protected static final java.lang.String TITLE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • JOURNAL_TAG

        protected static final java.lang.String JOURNAL_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • PUBMED_TAG

        protected static final java.lang.String PUBMED_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • MEDLINE_TAG

        protected static final java.lang.String MEDLINE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • COMMENT_TAG

        protected static final java.lang.String COMMENT_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • FEATURE_TAG

        protected static final java.lang.String FEATURE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • BASE_COUNT_TAG

        protected static final java.lang.String BASE_COUNT_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • FEATURE_FLAG

        protected static final java.lang.String FEATURE_FLAG
        Deprecated.
        See Also:
        Constant Field Values

      • START_SEQUENCE_TAG

        protected static final java.lang.String START_SEQUENCE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • END_SEQUENCE_TAG

        protected static final java.lang.String END_SEQUENCE_TAG
        Deprecated.
        See Also:
        Constant Field Values

      • FEATURE_LINE_PREFIX

        protected static final java.lang.String FEATURE_LINE_PREFIX
        Deprecated.
        See Also:
        Constant Field Values

    • Constructor Detail

      • GenbankFormat

        public GenbankFormat()
        Deprecated.

    • Method Detail

      • readSequence

        public boolean readSequence​(java.io.BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener listener)
                     throws IllegalSymbolException,
                            java.io.IOException,
                            ParseException
        Deprecated.
        Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. The sequence read in must be in Genbank format.
        Specified by:
        readSequence in interface SequenceFormat
        Parameters:
        reader - The stream of data to parse.
        symParser - A SymbolParser defining a mapping from character data to Symbols.
        listener - A listener to notify when data is extracted from the stream.
        Returns:
        boolean True if there is another sequence in the file; false otherwise
        Throws:
        IllegalSymbolException - if it is not possible to translate character data from the stream into valid BioJava symbols.
        java.io.IOException - if an error occurs while reading from the stream.
        ParseException

      • writeSequence

        public void writeSequence​(Sequence seq,
                          java.io.PrintStream os)
                   throws java.io.IOException
        Deprecated.
        Description copied from interface: SequenceFormat
        writeSequence writes a sequence to the specified PrintStream, using the default format.
        Specified by:
        writeSequence in interface SequenceFormat
        Parameters:
        seq - the sequence to write out.
        os - the printstream to write to.
        Throws:
        java.io.IOException

      • writeSequence

        public void writeSequence​(Sequence seq,
                          java.lang.String format,
                          java.io.PrintStream os)
                   throws java.io.IOException
        Deprecated.
        use writeSequence(Sequence seq, PrintStream os)
        writeSequence writes a sequence to the specified PrintStream, using the specified format.
        Specified by:
        writeSequence in interface SequenceFormat
        Parameters:
        seq - a Sequence to write out.
        format - a String indicating which sub-format of those available from a particular SequenceFormat implemention to use when writing.
        os - a PrintStream object.
        Throws:
        java.io.IOException - if an error occurs.

      • getDefaultFormat

        public java.lang.String getDefaultFormat()
        Deprecated.
        getDefaultFormat returns the String identifier for the default format.
        Specified by:
        getDefaultFormat in interface SequenceFormat
        Returns:
        a String.

      • addParseErrorListener

        public void addParseErrorListener​(ParseErrorListener theListener)
        Deprecated.
        Adds a parse error listener to the list of listeners if it isn't already included.
        Specified by:
        addParseErrorListener in interface ParseErrorSource
        Parameters:
        theListener - Listener to be added.

      • removeParseErrorListener

        public void removeParseErrorListener​(ParseErrorListener theListener)
        Deprecated.
        Removes a parse error listener from the list of listeners if it is included.
        Specified by:
        removeParseErrorListener in interface ParseErrorSource
        Parameters:
        theListener - Listener to be removed.

      • BadLineParsed

        public void BadLineParsed​(ParseErrorEvent theEvent)
        Deprecated.
        This method determines the behaviour when a bad line is processed. Some options are to log the error, throw an exception, ignore it completely, or pass the event through.

        This method should be overwritten when different behavior is desired.

        Specified by:
        BadLineParsed in interface ParseErrorListener
        Parameters:
        theEvent - The event that contains the bad line and token.

      • notifyParseErrorEvent

        protected void notifyParseErrorEvent​(ParseErrorEvent theEvent)
        Deprecated.
        Passes the event on to all the listeners registered for ParseErrorEvents.
        Parameters:
        theEvent - The event to be handed to the listeners.

      • getElideSymbols

        public boolean getElideSymbols()
        Deprecated.

      • setElideSymbols

        public void setElideSymbols​(boolean elideSymbols)
        Deprecated.
        Use this method to toggle reading of sequence data. If you're only interested in header data set to true.
        Parameters:
        elideSymbols - set to true if you don't want the sequence data.